Very Low Numbers of Significant Genes for Knockouts

[sojichld]

Hello,

We have used your package to run tests on a few datasets and having issue getting very few significant genes for total knockouts, and one or zero for the adjusted P value. Is this expected, or are there any specific suggested parameters that would yield more informative results?

Additionally, is there any directionality in the predictions? For example can we determine if something is up or down regulated by a positive or negative z score?

Thanks